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Author Topic: IMEP #132 Sapropel Linked to Shell and Finfish Disease  (Read 1486 times)
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« on: October 22, 2023, 03:13:39 PM »

IMEP #132
Sapropel Deposits Linked to Shell and Finfish Disease
“Understanding Science Through History”
The Danger of a Warming Planet – The Rise of Vibrio Bacteria
Blue Crabbers and Shellfishers Urged Caution in High
Heat Organic Deposits – This is a delayed report September 2019 – January 2021
Viewpoint of Tim Visel No Other Agency or Organization
Tim Visel retired from The Sound School June 30th 2022
Thank you, Blue Crab Forum™ for posting these habitat papers
Over 300,00 views to date

A Note from Tim Visel

It might be very hard for some blue crabbers to read this report – as it contains some information that will challenge perhaps some beliefs and values about estuarine habitats at the same time confirm hundreds of observations made by crabbers and inshore fishers themselves.  This report is not peer reviewed, nor is it funded by grants – it is a free of the often mentioned “funding effect” a research bias that has descended amongst the fisheries research community like a medieval plague – my view.

I strive to bring forward the best – accurate information I can and when I state an opinion I bracket or end – with my view – and welcome discussion and comments. 

The support of the Blue Crab Forum™ and the many comments/reads are very much appreciated and hope this educational effort will help many students to look at our marine environments with a viewpoint of both today and yesterday – our fisheries history.  This is especially critical as our planet continues to warm.  I find that the fisheries history/climate perspective has been absent until the Mackenzie – Tarnowski NOAA Marine Review article in 2018.

In 2018, see NOAA press release October 25 “Commercial Shellfish Landings Decline Likely linked to Environmental Factors, Not Overfishing” broke the ice on this topic.  This report links the change in shellfisheries to the phase of the NAO – something that John Hammond mentioned several times in my meetings with him while on Cape Cod 1981-1982.  It was Dr. Mackenzie who in 1987 gave me support of my first attempt to do a habitat history review.  (See Appendix #1 Letter of September 15, 1987 – East River Oyster Study in Guilford, CT.  This habitat history was the basis of IMEP #81: Oyster Bed History for Guilford CT 1848-1988, posted December 28, 2020, The Blue Crab Forum™ Fishing, Eeling & Oystering thread).

The absence of a climate history (at least what we have) has led to many failed restoration attempts.  In the 1970’s I helped salmon culture efforts in New England – with one facility in Old Lyme, CT deciding to move to colder waters.  The waters here were warming beyond the biological limits of this cold water species.  The decline of the brook trout was so severe in the 1900’s that heat tolerant rainbow and brown trout were introduced to many New England streams had warmed beyond biological limits of this cold stream species.  (See IMEP #89 The Fall of New England Brook Trout 1880-1920 posted June 17, 2021 Blue Crab Forum™).
I have mentioned several times the impact of the NAO and warm water street runoff as raising water temperatures.  This can have an immediate killing effect on brook trout.  Brook trout, when subjected to 82oF water can only live about an hour.  A negative NAO produces weak westerlies and warmer temperatures.  This is time that Long Island Sound temperatures were so high that one month later – August 12, 2012 water temperature was 76.7 degrees and caused the shut down of our nuclear electricity plant in Waterford, Connecticut to shut down.  The August 13, 2012 New York Times article by Matthew L. Ward had this statement,

“A reactor at the Millstone Nuclear Plant in Waterford, CT has shut down because of something that its 1960’s designers never anticipated, the water in Long Island Sound was too warm to cool it.”

A long positive phase of the NAO (in the 1960s the NAO was in a negative phrase) had vanquished the lobster but welcomed the blue crab once again.  At the turn of the century this reversal had happened before. 

The period 2006 to 2012 time that Connecticut blue crabbers enjoyed catches not seen in Connecticut for decades (See Adult Blue Crab Enter CT River in Huge Numbers, posted August 24, 2012, The Blue Crab Forum™ Northeast Crabbing NE Crabbing Resources thread).

The absence of fisheries history (fisher catches and cycles) is now a reason to include mandatory historical reviews of all relevant habitat research – our fisheries records from the last century or before if possible – my view, Tim Visel.  This is so important as hot marine composts hold several disease-causing pathogens.

We cannot allow what happened around eelgrass/sapropel research to happen again – sulfide can kill eelgrass so can a building marine compost which contains slime molds and vibrio bacteria.  Higher temperatures support increased fish and shellfish disease, including bacteria pathogens.

I mentioned this concern to the EPA Long Island Sound Study and continue to caution about sapropel – the blue-black often greasy marine compost (first one in 2012).  This was my viewpoint and did not in any way represent EPA or the Habitat and Stewardship committee I belong to currently.

After many years and since 2012 I have not been successful in gaining attention to the sapropel chemistry and concerns of eelgrass.  Sapropel habitats and now it appears the subject of a new long-term view and possible scientific review.  Sapropel tends to build up in long hot periods – in areas of shallow water and slow tides.  Fishers and crabbers experience these organic deposits – they fish in them and walk across them.  Sapropel is the sticky mud or “black mayonnaise” ooze mentioned in many of my habitat and environment newsletters.  Although it can dramatically change estuarine habitat by direct suffocation (eelgrass/sapropel covers bottoms – suffocating clams and oysters below) but is also the culture media – food for a series of sulfate reducing bacteria now linked to seafood disease – the vibrios shell dissolvers and flesh necrotizing strains of vibrios that now appear to be impacting blue crabbers as well.  This health caution carries an important temperature message – in cold water with good tidal flows the surface of sapropel contains different bacterial strains – ones that use oxygen to breath – when it gets hot and oxygen is short or “limiting,” different types of bacteria now feast upon this organic matter (northern areas primary leaves but in southern areas large amounts of manure) slowly digesting it and beginning very different biochemical processes.  These are the sulfate bacteria.  As sapropel “rots” in high heat the sulfate bacterial strains take over and as they do emit sulfides – the sulfur smells associated with blue crab jubilees – when they occur the sulfate bacteria have “won” they now dominate in these organic bottom deposits.  Sealed from oxygen sapropel is formed hosting the dangerous sulfate bacterial strains – the desulfovibrio series – some of the historic infamous strains include those causing much death in hot periods a century ago such as Vibrio cholerae - shortened to cholera the turn of the century. 

The desulfovibrio bacterial strains are some of the most dangerous and they love the heat – their oxygen requiring foes the “good” bacteria die off and they utilize sulfate as an oxygen source.  For these sulfate reducing bacteria there will never be an oxygen shortage – sulfate compounds are extremely abundant in sea water.  The eelgrass/sapropel deposits harbor these bacterial strains and as eelgrass/sapropel habitats grow so does these dangerous pathogens. 

Some of the most mentioned vibrio bacteria mentioned during the very hot years 2008 to 2012.  (Since 2012 we have had a slight cooling from some harsh long snow filled recent winters) are Vibrio parahaemolyticus and Vibrio vulnificus.  Blue crabs are known to contain these bacteria since the 1980’s found first in southern areas and gradually moved north as this recent warm period continued to strengthen (See Incidence of Vibrio Species Associated With Blue Crabs Collected From Galveston Bay Texas.  (JW Davis and RK Sizemore Applied Environmental Microbiology May 1982 – Pages 1092 to 1097) and more recently Prevalence of Vibrio parahaemolyticus and Vibrio Vulnificus in Blue Crab, Sea Water And Sediments of the Maryland Coastal Bays, (C. Rogers et al., Journal of Applied Microbiology, 2014 Oct., pg. 1198-1209).

A Missing Piece of Public Policy

No matter the reason this energy/temperature habitat succession pattern is consistent along our coasts.  What makes these habitat case histories so important is the records of habitat observations to habitat successional events.  All these case histories describe the increase of organic humus – termed “black mayonnaise” but more aptly termed “sapropel.”  It is the rise and fall of sapropel which governs habitat succession in shallow areas one most likely to contain shellfish.  This composting feature is rarely mentioned today in estuarine reports.  (Note this appears to be changing – Massachusetts has a recent report titled in regards to Wellfleet Harbor dredging, titled “Black Mayonnaise” in Wellfleet Harbor.  What is it and where does it come from” (Center for Coastal Studies Province town Herbert Marine Laboratory Provincetown, MA).

The report describes the buildup of organic ooze 8 to 12 feet deep.  On page 1 is found this segment, my viewpoint (  ) Tim Visel:

“The material analyzed was high in organic matter (derived from marine vegetation and low in species diversity compared with data sample at a control station at “The Gut” and data previously collected in 2015.  A total of 13 species were found, 6 of which are worms common in silting, low oxygen sediment.”  (Terrestrial and marine plants may both form marine composts – T. Visel).

The source of black mayonnaise (termed black custard Mittermayr, 2020) was found to be iron disulfide FeS2 or iron pyrite and sapropel on page 13.  It is the same description that was given by Dr. Donald Rhoads of Yale University given at a NOAA-EPA Estuary of The Month Seminar Series No. 3, May 10, 1985.

The Seminar Proceedings published January 1987 – Paper titled The Benthic Ecosystem Dr. Rhoads provides this explanation of sapropel in low oxygen waters – pg. 52 of a May 10, 1985 Workshop Proceedings has this section, referencing oxygen levels,

“Below concentrations of 0.1 ml/liter, metazoans do not do well and only anaerobic bacteria, along with some nematodes (worms) are found in abundance.  Underlaying the dysaerobic and anaerobic water are typically found organic – rich black (i.e., sulfidic) muds that are termed sapropels.  These are rich in iron monosulfides.  The physical properties of these mud are distinctive and the best description that I have heard of them is they are like a “black mayonnaise” Dr. Donald Rhoads Yale University Department of Geology and Geophysics – 1985.

In the historical records you find reports of “black water deaths” or “foul bottoms” now linked to sapropel and sulfate reduction (high sulfides) in it (Jamaica Bay New York).  Sapropel is now being linked to the vibrio bacterial series – including lobster shell disease and winter flounder fin rot.  I now strongly suspect changing habitat conditions from sapropel to enhancing swimmers itch – a parasite worm vectored by the mud snail and waterfowl that feast upon submerged aquatic vegetation and now the oyster disease MSX the Hammonnasset River in the 1980’s.  Some recent papers have linked pulp/paper mill refuse as increasing the winter flounder parasite, but in our area (and in many New England Bays) the primary organic food for these parasites is tree leaves.  (Clinton Harbor in the 1980’s had high levels of this winter flounder parasite.  In the Dardanelles (Clinton CT) case when it is closed leaves accumulate and rot in heat causing sapropel to build up with sulfur or rotten egg hydrogen sulfide smells.  When open (after 1938) the harbor has greater tidal oxygen exchange and sapropel lessens. 

Dredging can rebuild habitats, and is a positive habitat restoring activity but because it is so opposite the policies of regulatory agencies in fact many times do not recognize the existence of sapropel (such as our state) but Rhode Island and Florida have recently launched “Black Mayonnaise” research programs in efforts to warn the public and to seek options regarding its removal or possible reuse as a thin layer deposit.  Up until the 1960s Connecticut once used hydraulic removal to spread liquid sapropel on marsh surfaces.  Once again exposed to oxygen it became a marsh/soil enhancement “dressing.”  This was part of the mosquito ditching effort.  This is an excerpt from The Shoreline Times, Nov 25, 1957 article – photo caption Alice Kelsey page 12 M (Hammonasset State Park).

“Ernest Lindquist and Frank Rettich are busy with a monstrosity of a machine which cleans out the ditches in the salt meadows of the State Park in work of the State Mosquito Control.  Ernest is keen about any type of machinery, so is having a fine time experimenting with the operation.  The flexible tubing was run into the ditch to such up the muck which was forced out onto the marsh.  Also working on the project was Albert Lindquist who has been employed with the state for 22 years, enjoying all the variety of outdoor work the job brings.”

Today thin layer deposit is often portrayed as a new technique.  It is not coastal farmers once harvested as a grass/hay “top dressing” (See IMEP #86-B: Oyster Fishers-Farmers Struggle Over Harbor Mud, posted May 20, 2012, The Blue Crab ForumTM Fishing, Eeling and Oystering thread and Appendix #6).

As for the closed Dardanelles inlet in Clinton Harbor the westerly edge of the barrier spit is under sulfate reduction from aerial photos like in a year or two it will breach into the Hammanosset River through the salt marsh – one good storm should do it.  This opening is consistent with some very old maps of the area which at times shows no Cedar Island at all, most likely then a subtidal sand bar which once occurred at The Niantic River visible only at low water.

The Sound School recently issued a second warning to researchers about sapropel – as the vibrio bacterial strains have been linked to the flesh necrotizing disease of blue crabbers.  Blue crabbers came in contact the most with high temperature sapropel as they fish in the shallows and get cuts.  Shellfish also can accumulate vibrio and the bacterial strains most concerning include camptobacter series which thrives in high heat.  Dave Carey of the CT Dept of Agriculture/Aquaculture Division during a vibrio outbreak in CT is quoted as stating. 

David H. Carey, Director of the State of Connecticut Bureau of Aquaculture in August 17, 2013, New Haven Register article has this statement,

“In the wake of illnesses, one action the State has taken is to recommend that growers for now only harvest shellfish grown in “very deep water” at least 20 feet deep at low tide because that water is cold enough to inhibit Vibrio growth Carey said.  The recommendation runs through September “Vibrio levels are much lower in colder, deeper water,” he said.

The increase in sulfate reducing bacteria appears to be directly related to the formation of sapropel.  We have two very warm (hot) periods to compare – the 1880’s to 1890’s and one century later 1980’s to 1990’s.  This is the bacterial change of a warming planet – my view, Tim Visel.

The Heat Brought Disease To Us As Well

The 1890s were those that saw the US economy recover from the financial crisis of 1873.  The roaring “90s” had the economy in growth and for New England the continued heat turned the stream of summer shore visitors now into a flood – for those who could afford it.  The building of cities and immigration caused eastern sea board communities to grow as well and with it the deadly scourge of tuberculosis.  In the 1850s you had a one in four chance of succumbing to this deadly disease in Europe and America.  A bacteria Mycobacterium tuberculosis was the source of this deadly contagion, a single sneeze could spread thousands of invective particles on moisture droplets.  Cities with dense populations were extremely susceptible and consumption as it was called then with those in living cities had the highest death tolls.

Some medical researchers soon discovered that people living in the country or shores areas did much better and fed into the existing belief of “bad airs” as Maisma theory of germ spreading disease.  Cool good airs were salt airs and the scientific community still held to “putrified airs” as a source of disease.  This soon turned the coastal summer visitors from a steady stream into a flood not only did the cooler lake and seawaters provide relief from killer heat waves.  These salt or mountain “airs” were now classified healthy.  A 1906 advertisement (pg. 93 Gimpses of Maine’s Angling Past Donald A. Wilson 2000).  Lists a trout fishing lodge Mount Kinen House “A Perfect Health Resort.”

With Cholera, Typhoid and the sweltering heat in crowded cities were the dreaded times of summer.  TB outbreaks occurred during the winter.  Those who could escaped these cities to spend time at the shores where shore breezes developed as inland areas heated and drew air inland – the cool “shore breeze.”

A German Doctor Robert Koch first identifies Mycobacterium tuberculosis in 1882 – identifies modes of transmission and details the highly contagious nature of disease – the scientific community dismissed the discovery as most still believed that TB transmission was genetic.  A climate connection to “TB” however would soon involve fishers.  New England Climate Conditions after 1864 turned colder.  The Boston Medical and Surgical Journal – May 3, 1906 has this section pg. 492. 

Dr. William Ogle has shown the fishermen, who are from the nature of their occupation, exposed to the greatest amount of moisture in the air and surroundings, have the lowest death rate from respiratory disease, and that occupations necessitating an indoor like the highest, where presumably they are more protected form dampness and the vicissitudes of weather.  The late Dr. Abbott of our State Board of Health conclusively demonstrated tuberculosis to be essentially an indoor disease and the outdoor treatment is our so-called damp and cold” (The 1906 New England Journal of Medicine, Vol. 154, Pg. 491).

The incidence of tuberculosis, an infectious bacterial disease primarily of the lungs, once called consumption, soared after 1898, as cities felt the burden of outbreaks resulting in the construction of sanatoria for “fresh air” after reports were circulated such as the above after 1906.  Sanatoriums were often built on lakes and by the sea.  The Catskills in New York became the location of the first sanatorium for the treatment of tuberculosis.  In 1930, the State Commission on Tuberculosis would purchase the Smith-Crimes estate in Waterford, CT and became a “Seaside Sanatorium” until the use of streptomycin made such establishments unnecessary.  For half a century, people with tuberculosis would seek out salt air, believing it had curative powers.  This belief of “salt air” continued far into the 1950s and 1960s.  The former Waterford estate is now scheduled to become a state park.

Dr. Edward Trudeau after contracting “TB” in 1873 moved to the Adirondack mountains were his health greatly improved – he investigates climate as a relief to this disease establishing a sanatorium on Saranac Lake (New York).  This is the climate period I term the great heat 1880-1920 which had New England warm to hot summers.  This is when people flocked to the shore to breath healthy “salt air” or fresh air.  This is when the Wilcox family of Stonington would find people on their property trying to get close to the sea (see Clinton Harbor and the Great Heat 2012) or states now building TB facilities on the shores (such as Seaside in Waterford, CT).

Later, pasteurized milk had eliminated M. Bovis as a strain that spread TB.  It was however Dr. Selman A. Waksman in 1943 – the same Dr. Waksman studying the bacteria in peat (IMEP #61-A (2017) who would break the strangle hold of TB grip on cities.   

According to a CPTV – American Experience Summary on Tuberculosis between August 1943 and October 1943 Dr. Waksman an expert on soils supervised then Rutgers student Albert Schatz researching Streptomyces, bacteria with fungal attributes observed that Streptomyces bacterium killed Tuberculosis bacillus – (later to be named Streptomyces griseus found in farm soil) and the start of a bacterial battle in the first step in many of reducing the scourge of “TB.”  We know that outcome as Streptomycin in sulfate.  Streptomycin kills gram negative bacteria like cholera. 

Damp moisture conditions would reappear again in cities to produce lung infections in the 1980’s known as Legionnaries’ disease.  This disease outbreak in 1976 was linked to a bacteria that thrives in warm moist conditions.  Legionella bacteria is gram negative and is treated with azithromycin. 

Sulfate bacterial reduction is as old as recorded time itself the smell of sulfide – that marshes were the source of “bad airs” then thought to be disease carriers.  The summer mists or fogs that mingled with sulfides and “marshes gases” were long known to coastal people – they smelled bad or foul and linked to disease.  What was happening to produce the bad smells or “Miasma” disease causing “night airs” what organic composting.  The ancient Greek word for pollution was Miasma.”

A History of Habitat Clocks

Many communities are working on projects that concern estuarine species, their habitats and reproductive capacity.  Perhaps now other species has come to the attention of habitat requirements than the eastern oyster and river herrings, each with a habitat history and cycles of abundance related to climate patterns.  Those patterns and catch statistics form part of a fisheries history – connected to habitat quality and capacity.  This is especially true for the American or eastern oyster Crassostrea virginica and the climate feature known as the North Atlantic Oscillation or NAO.

It is apparent however that these historical aspects are missing from many current estuarine discussions and reviews – not only a lost opportunity for knowledge itself but redirects important future research efforts away from heat induced habitat succession.

The importance of habitat succession has been largely overlooked in the estuarine habitat field (my view) – brought forward in past reports, records and accounts.  Some of my modest investigations have indicated patterns of habitat change that influences fish (droughts) and shellfish (hot seawater) populations.

In fact, the study of sapropel may answer not only fish and shellfish population questions but provide how dangerous a warming planet is to shore residents and those that fish in shallow waters – the change of bacteria.

In many of my habitat papers, I take into account some of the comments made to me by a small boat workshop attendees - while employed by Cooperative Extension Services in the 1970s and 1980s.  I was very fortunate to have worked at the University of Rhode Island, Massachusetts and Connecticut, and thousands of small boat fishers that attended often took the time to share habitat and fishing experiences with me.  By the mid 1980s I had finished a short stint with the Cape Cod Cooperative Extension Service, and had met Mr. John “Clint” Hammond of Chatham who urged me to continue to look at fisheries history but combine it with temperature and energy – himself a retired oyster grower.  He especially was concerned about the sulfur cycle, and the build up of “humus” (I termed black mayonnaise) over oyster beds as a “habitat reversal” a term signifying habitat succession.  The concept of a species habitat “clock,” habitat history and habitat successional aspects came in a large way from my meetings with Mr. Hammond in Chatham.  It was Mr. Hammond who pointed me to the 1880-1920 period in New England, I often call the “great heat.”  He was also the one who thought my knowledge of the sulfur cycle could use some “improvement.”  I still have some of the sulfur cycle and rice culture papers he gave me.

The more recent exclusion of fisheries history is unfortunate – many coastal towns have extensive fishery reports left by the US Fish Commission reports of the 1880s and 1890s.  The rise and fall of fisheries upon review have a direct climate and energy link and a complete (unbiased) environmental fisheries history is missing from many coastal studies (my view).  Most often the rise and fall of inshore fisheries is attributed to misuse, pollution or overfishing when in fact those explanations lack the depth of research and at times even the “science” to sustain them. 

It is science of sulfur and sulfide tolerant organisms that Mr. Hammond that so concerned him at the end of his oystering career.  The marine compost frequently termed black mayonnaise but more aptly designated sapropel was linked to large oyster losses.  Often these dead oysters were stained black.

Many coastal fishers have not heard the term sapropel – the reduction of organic matter in low or no oxygen.  This bacterial process governs the purging of ammonia and in heat the byproduct of sulfide.

Ammonia tends to increase in depth as ammonia oxidizers died off.  Ammonia has a pH of 12 and alkaline conditions may protect the protein shells of cysts.  After a storm these cysts are redistributed into these oxygen zones where organic acids can break these shells – (coats) releasing activated cysts.  It is known that sapropel sulfide can be converted to sulfuric acid.  (See Acid Sulfate Soils of the US Mid-Atlantic Chesapeake Bay Region July 8, 2006 Delvin S. Fanning University of Maryland College Park) soil samples from a marsh/creek in Maryland when exposed to hydrogen peroxide generated sulfuric acid. 

There has been a reluctance to term this sulfide rich organic matter as a sapropel deposit – I believe due to the negative habitat implications including its ability to culture many of the desulfovibrio bacterial series (linked to shellfish and finfish benthic disease) the flesh and shell dissolvers also, the sulfate reducing bacteria role in complexing heavy metals (even mercury compounds).  In addition, as by product respiratory process generation of ammonia and sulfides.  Most likely the most infamous desulfovibrio series known to the public is the one called vibrio cholera or cholera for short.  This material is a largen negative habitat health indicator for our shoreline.  Due to ethical concerns (and a lack of response from CT state and federal agencies) areas of sewage outfalls that have high organics or areas with a source of natural organic sources (such as leaves, forest duff or street water organics) can be a source of human vibrio infection.  Sapropel deposits in high heat have now been linked to high ammonia generation starting cultures of Harmful Algal Blooms (HABs) primary source of sulfides in embayment, higher heavy metals especially toxic aluminum concentrations.  Because of its ability to complex heavy metal ions it is used in Europe as a bioremediation process to clean heavy metals spills.  Additional concerns have been expressed that the ammonia levels generated from this organic reduction process was not included in nitrogen TMDL calculations.  This was confirmed when I attended an EPA sponsored workshop at the University of Connecticut Avery Point Campus in July 2016.

A further concern is that for four decades the public has been informed about the value of a subtidal habitats and a bias toward dredging them as a negative habitat environmental activity.  Because of that bias, I believe a series of terms have come about that refers to sapropel – but does not name it directly to perhaps avoid possible regulatory review – that is clearly evident in the last EPA – Army Corps of Engineers Dredge Management report.  My comments are the only ones that reference sapropel.  Many Natural Army Corps Engineer Reports refer to sapropel (marine compost) as acidic sulfate soil only after it breaks the surface below the surface it is termed sediment or “unsuitable fines.”  Sapropel is not mentioned nor its long historical use as a marine compost natural fertilizer in recent Long Island Sound Dredge Material Management reports.

Sapropel is a natural marine compost (humis) that holds hundreds of strains of bacteria that can live in low to no oxygen conditions.  In heat and low oxygen conditions it can build up quickly and occur in shallows the 10 feet or less in critical seafood habitat (nursery) zones.  In Europe sapropel is currently used overseas as a natural “green” renewable fertilizer (high in carbon) and a bio remediation chemistry agent, it is considered a valuable substance.  Historically our state harvested sapropel called marine muds or mussel mud from rivers as a soil.  When exposed to oxygen they can become acidic.  Analysis was performed at the New Haven Agriculture Experiment Station – who suggested oyster shell as a pH Buffer.  We need to recognize sapropel for the good as well as the negative environmental – mislabeling or misrepresenting these deposits I consider a form of science (research misconduct) and I feel deserves immediate review.

Previous attempts to engage state officials about disease cysts in sapropel has had little response, perhaps a review of sapropel nourishment (compost) at the federal level may gain a greater public awareness.
Shellfish, Finfish Disease Pathogens Linked to Sapropel (Black Mayonnaise) Deposits

In February 2016, The Sound School issued a second warning about Sapropel (Black Mayonnaise) harboring dangerous Vibrio bacteria (see Blue Crab Forum Special Report #1 Feb 15, 2016 Northeast Crabbing Resources).  Sapropel upon review of historical documents may hold fish and shellfish disease cysts - buried in it.  These not only include red tide (see Mumford Cove red tide cyst account IMEP #97 part I posted October 5, 2021) but also upon cysts for harmful algal strains, red tide, and fish parasites.  Upon review it is beginning to become very apparent that sapropel itself has a climate link – it accumulates in times of reduced storm energy (or tidal restrictions) and heat.  It is the periods of heat that many diseases and harmful algal blooms thrive in or adjacent to sapropel.  The accumulation of this organic deposit and sulfur reducing bacteria now appears to have Vibrio species disease links.  At the 1990s warmed and the presence of sapropel a humus deposit undergoing sulfate reduction by sulfate reducing bacteria increased it generated large amounts of sulfides (the rotten egg smell) and ammonia – measured by extreme high pH just above sapropel deposits.  It is the high ammonia in shallow poorly flushed bays that appear first in New York coves and bays from dunk wastes (large amounts of ammonia) a necessary nutrient for the harmful brown algal strains of Long Island New York.  Many coastal fishers called sapropel “Black Mayonnaise” the petrification of organic matter by bacteria who do not require oxygen – the sulfur reducing bacteria.
Cysts are found in high organic deposits some of this research occurred in New York.  Surface studies had neutral to slightly acidic pH but deeper samples mores acidic.  Core samples often show the results of sulfate reducing bacteria by an enriched sulfide residues.  Sulfide/Ammonia profiles can be found in the water but sulfide is more reactive especially in soils containing iron.  Ammonia can form below thermoclines (temperature boundary layers) in the summer and any cysts falling into it can remain dormant.  A sudden storm can put oxygen into the benthic community and cause a similar organic acid flash.  This low pH event can lead to the reactivation of these once buried cysts.

In Connecticut one of the coves found to harbor red tide cysts was Mumford Cove also found to have deep accumulations of sapropel then termed black facies, see CT CW F 266-R (Post Glacial Stratigraphy and Rates of Sediment Accumulating In Three Small Connecticut (Coves 1993).

Environmental conditions, storms, floods and temperature appears to trigger mechanisms from sapropel – sulfuric acid washes after preexposure to oxygen (noticed by New England Agricultural Experiment Stations when farmers harvested sapropel for fertilizer) that can on occasion dissolve metal crab traps.  These acidic washes can lead to fish kills (eels in the Herring River Wellfleet Cape Cod) and free “aluminum” in such levels as to create toxic conditions.  Sulfides in deep deposits in connection with ammonia generation may trigger the busting of cysts leading to disease (MSX) and blooms of harmful algal strains themselves that produce toxins.  Blooms and diseases after occur first in the shallows, subject to warmer sea water temperatures, low or restricted flushing and the accumulation of black mayonnaise (sapropel) over cove bottoms.

It is the periods of heat that oyster diseases thrive – it is also when sapropel accumulates.  The presence of oyster diseases were noted in US Fish Commission reports happened in southern areas (warmer) as the area (New England) went into the warm period in the late 1880s.  US Fish Commission Surveys of the 1890s (Long Island Sound) found the bottom with a foul smelling black muck – most likely a sapropel.

Many of the fish kills of the last century were blamed on pollution but now after reviewing the historical records disease and blooms most likely caused much of the loss – also mentioned softer or muck filled bottoms fishers now term Black Mayonnaise.  A strong storm may dislodge long ago buried cysts – meeting the warm and ammonia rich waters now proliferate.  The storm or hurricanes may have caused a series of events that expose long ago buried cysts buried in sapropel deposits followed by a flush of sulfuric acid that may release iron bound in it – the iron that turns these deposits black – the sulfuric acid and ammonia availability might be the trigger once these cysts are “turned up” into water column.   

New York had been a leader in studying the Presence of Brown Tide Cysts – as it contains many bays that are shallow and obtain organic residues.  (See Estuaries Vol 28 #5 pages 726-749 Gobler et al “Review of the Causes Effects, and Potential Management of Harmful Brown Tide Blooms Caused by Aureocuccus anophagefferens.”

Coastal Lagoons – Critical Habitats of Environmental Change
“Blooms in Lagoons” Gilbert et al pg. 91.  McIntyre I.G.R. Rutzler and I.C. Feller 2004 – The Twin Cays Mangrove ecosystem, Atoll Research Bulletin Nos 509-530.

Evolution of Primary Producers In The Sea – Kallowski et al., 2011
“The cyst-forming species are of particular importance because of their ability to appear in the sudden, high density blooms known as red tides, (or mahogany or “brown” tides) and the role of cysts in the fossil record.  The cysts can lie dormant in on shore sediments for years until conditions favor germinating and suddenly a huge population can appear, literally overnight.”

During the summer of 1997, a series of fish kills occurred in the small shallow tributaries of Chesapeake Bay and some deeper coastal bays.  The causation agent for these fish kills was determined to be the toxic dinoflagellate Pfiesteria.  “This is complex organism can reside as a cyst in the sediments of estuaries or as a non-toxic dinoflagellate.  These cysts can turn into toxic producing cells when conditions are right” (warm water, high nutrient loads, moderate salinity, poor flushing).  Pfiesteria has 24 different life stages – EPA condition of the Mid-Atlantic Estuaries, EPA 600-R-98-147, Nov. 1998, pg. 31. 
The increase of parasites was to impact fish as well Clinton Harbor and is a good case study.  There is little doubt that increasing temperatures assist diseases and parasites. (My view, Tim Visel)

Glugea stephani – microsporan is linked to flounder decline Wayne Castonquay 1988 M. S. Thesis University of Connecticut 38 pages.  The Occurrence of Glugea Stephani Induced Microsparidiossis In Long Island Sound Winter Flounder.

Appendix #1

The Sound School Regional Vocational Aquaculture Center
Third Black Mayonnaise (Sapropel) caution 2018

It is becoming apparent that the accumulation of Black Mayonnaise is more than a detrimental habitat accumulation of organic matter but a potential vector for shellfish and finfish disease, a nutrient base for toxic or harmful blooms and may also trigger more toxic diseases such as red tides and MSX.  These toxic life forms may after reviewing historical literature have a sulfide ammonia activating sequence that lies dormant until heat creates condition of sulfide toxicity and extreme alkaline conditions.  These also appears to be a correlations between the accumulation of Black Mayonnaise (Sapropel) and harmful algal blooms in poorly flushed bays – high ammonia levels and the presence of hydrogen sulfide (bad smells).  Many of these toxic impacts are biological – parasites, toxic blooms, and also bio chemical – large fluctuation of pH, accumulations of heavy metals and the release of aluminum.  Many of these toxic conditions are the result of vibrio bacteria – and appear to be climate related – occurring in organic deposits undergoing sulfate reduction Vibrio bacteria are gram negative and can be considered dangerous in high heat.

Appendix #2
Shellfish Closures in Massachusetts: Status and Options
Edited by Alan W. White
Lee Anne Campbell
Woods Hole Oceanographic Institution
Woods Hole, Massachusetts 02543
September 1989
Technical Report

Funding for the workshop and preparation of this report was provided by NOAA National Sea Grant Program Office. Department of Commerce. under Grant No. NA-86-AA-D-SG090. Woods Hole Oceanographic Institution Sea Grant Project Nos. M/0-2 and A/S-10-PD.
Reproduction in whole or in part is permitted for any purpose of the United States Government. This report should be cited as: Woods Hole Oceanog. Inst. Tech. Rept., WHOI-89-35. Approved for publication; distribution unlimited.
Approved for Distribution:
David A. Ross, Chairman
Department of Geology & Geophysics

Robert A. Duncanson
Water Quality Laboratory
Town of Chatham
Chatham, MA 02633
Dale L . Saad
Town of Barnstable Health Department
Hyannis, MA 02601

The use of bacterial species as indicators of the sanitary quality of water had its origins in the early part of this century. The indicator concept was begun as a protective measure for potable water supplies in response to widespread outbreaks of waterborne diseases such as typhoid and cholera.
The use of bacterial indicators in the shellfish arena began in the 1920s following several outbreaks of typhoid linked to oysters. Since the introduction of bacterial standards for both shellfish growing waters and market samples, the incidence of shellfish-borne disease has declined. The question thus becomes why should consideration be given to a change in the indicator system which appears to have been working adequately for over 60 years?
The answer to the question posed above is multifaceted. Although the incidence of classical shellfish-borne diseases (typhoid and cholera) have declined, there are increasing numbers of disease outbreaks attributed to shellfish. This would indicate that the pathogenic agents involved in these more recent outbreaks are not the classical pathogens which the original indicator system was meant to warn of. Indeed, in many recent outbreaks other bacteria, such as Aeromonas hydrophil!!, Vibrio parahemolyticus and V. vulnificus, have been the cause. This, combined with advances in microbiological techniques and a greater understanding of microbial ecology, has opened to question some of the early assumptions upon which usage of the current indicator is based.

Indicator Characteristics

In order to evaluate the current indicator and any potential alternative, it is necessary to understand what the indicator should be doing. As commonly defined, a water quality indicator (potable, recreational or shellfish) "should indicate the possible presence of more serious pathogens." This definition implies a relationship between the indicator and the pathogen. A "good" indicator is said to have the following characteristics: 1) it should be consistently and exclusively associated with the source of the pathogen(s), 2) it should be present in numbers, relative to the pathogen, high enough to reflect accurately the potential presence of the pathogen, 3) it should approach the resistance to environmental stress and disinfection of the most resistant pathogen, 4) it should not multiply in the aquatic environment, and 5) it should be countable by easy, inexpensive methods with precision, accuracy and specificity. It is becoming evident that the currently used indicator system for shellfish sanitation may be flawed in meeting one or more of the above requirements.

The Current Indicator

The current standards for the sanitary safety of shellfish rely on the use of the fecal coliform indicator. Fecal coliform is a group comprised of at least two bacterial species, Escherichia coli and Klebsiella spp. Until recently it was assumed that the fecal-coliform test, as recommended, measured organisms whose origin was the fecal material of warm-blooded animals. However, studies have shown that some Klebsiella spp. can multiply to high levels in carbohydrate-enriched waters in the absence of fecal wastes. Other studies have shown that the resistance of coliforms to disinfection and environmental stress may be much lower than that of the pathogens, especially the viruses. There is also mounting evidence that some coliforms may multiply in, or at least survive for extended periods in, some aquatic environments such as marshes and sediments. This limited discussion of some of the potential problems with the current indicator system should result in at least an examination of potential alternatives.
Probably the simplest solution for determining the sanitary quality of water would be to look for the pathogen(s) of concern. Currently this is not done for several reasons. Fecal waste may contain an increasing list of potential pathogens depending on the population contributing and advances in laboratory techniques. At least 114 types of human enteric viruses have been identified in sewage. A further problem is that many of the pathogens of concern can only be detected by time-consuming, expensive and labor-intensive methods. Many of the viral agents have yet to be identified and others cannot be grown in the laboratory.

Alternative Indicators

This, then, brings us back to the need for an indicator of the potential presence of the pathogen. Alternatives to the current indicator system can be divided into four categories: bacteria, yeasts, phage/viruses and chemicals.

Included in the bacteria list are organisms such as E. coli which was the original indicator of the 1900s. Methodological problems forced tests for E. coli to be broadened into the total coliform and fecal-coliform groups. E. coli, the only coliform exclusively associated with the gastrointestinal tract, thus had its effectiveness as a fecal-waste indicator lessened by being grouped with organisms which had non-fecal sources. Recent advances have produced rapid, easy, inexpensive and specific methods for enumeration of E. coli. E. coli, along with Enterococci, a more fecal-specific component of the fecal streptococci, have recently been recommended by the Environmental Protection Agency (EPA) as the indicators of choice for recreational waters because they correlate with illness better than do total or fecal coliforms.
The fecal coliform/fecal streptococci ratio gained a lot of attention as a potential indicator system when it was shown that human fecal waste produced a ratio greater than 4.0 while other warm-blooded animals produced ratios less than 0.7. Unfortunately, further research showed that the fecal waste of gulls, frequent inhabitants of shellfish waters, often produced ratios in excess of 4.0.

Several anaerobic bacteria have potential as indicators. One, which has been used extensively as a conservative tracer of sewage sludge, is Clostridium petfringens spores. Its usefulness as an indicator of recent pollution and the presence of pathogens is limited due to the extended survival of the spores. Other anaerobic bacteria which may be useful alternatives are Bifidobacteria spp. and Bacteriodes fragilis. The former has a specific association with the fecal waste of mammals, and the latter has been detected in 100% of the human fecal samples examined. Problems with methodology must be overcome before these species can be properly evaluated as indicators.

Other potential bacterial indicators include Vibrio parahemolyticus, Aeromonas hydrophila and Pseudomonas aeruginosa. V. parahemolyticus is a normal inhabitant of marine waters. Although this organism appears to respond to nutrient loading resulting from sewage disposal, its ability to grow in the marine environment limits its use as an indicator of pathogens. Aeromonas responds to nutrient loading in fresh waters and, like Pseudomonas, can multiply in aquatic environments, thus limiting its usefulness. Pseudomonas is used in some areas as an indicator of the sanitary quality of swimming pools and hot tubs.

Candida albicans, a member of the yeast group, has also been studied as a sewage indicator. Initial results are not promising as it has been detected in significant numbers in pristine areas and not found in areas known to be impacted by sewage.

The phage/virus group contains three classes of potential alternative indicators: Bacteriophages (bacterial viruses), Coliphages (bacterial viruses which specifically infect E. coli) and the Enteroviruses themselves. The problems with the latter group have been discussed earlier. By being viral in nature, the first two overcome one of the major arguments against bacterial indicators, i.e., they may not behave like the viral pathogens. More research is needed to see how well phages simulate enteric viruses. Several methods have been developed for the phages which will allow these organisms to be evaluated as indicators.

The final potential alternative indicator to be discussed is the chemical coprostanol. This compound is present in human fecal material and has been utilized as a tracer of sewage sludge. However, as an indicator for routine use, several problems must first be overcome. The methodology is expensive and time consuming. There are also concerns over some natural sources of coprostanol in the environment.


In summary, there are several potential alternatives to the currently used fecal coliform indicator system for the sanitary quality of shellfish growing waters and the shellfish themselves. The current indicator system will not change quickly since all of the alternatives have important questions which must be answered. Information must be collected on: a) the human fecal specificity of any alternative, b) some correlation, preferably positive, between the alternative indicator and the risk of human disease transmission from consumption of the product, c) the potential for disease transmission via the shellfish route from sources other than human fecal waste (i.e. waterfowl) and whether the alternative will protect against that risk, d) the survivability and transport characteristics of the alternative relative to the pathogen(s) of concern.

A final point for consideration is that a change in the existing indicator system to one which overcomes some of the current problems may not result in major changes in the way the shellfish sanitation program operates or its impact on the resource.


Brown Tide Cysts Linked To New York Bay Flushing
Sapropel Linked to Shellfish and Finfish Diseases and Parasites

It is becoming evident that organics provide habitats for many organisms that have temperature and energy triggers. These are increasing found to be harmful to seafood and US.  These diseases parasites are now associated in soft ammonia rich organic deposits.  The slower the currents or deeper the organic deposits the apparent higher number of diseases and parasites. Influence of nutrients and climate on the dynamics and toxicity of Alexandrium fund dense blooms in a New York estuary – Theresa Hattenrath 2009 found that cysts concentrations (cysts cubic) centimeter in Northport Huntington Bay in 2008 were over 700 cysts (poorly flushed) while at the Bay Mouth only 0 to 10 cysts pg. 35 (where flushing rates are better).  Cyst densities were much less.

And Hattenrath Lehman et al in a recent survey in 2016 of Shinnecock Bay that cyst surveys of Old Fort and Pond had over 500 cysts in just one cubic centimeter (of C. Polykakoides).

Old Fort Pond is an indented portion of Shinnecock Bay Long Island and could be described as a low energy high organic area that most likely contains an oxygen poor organic layer.  Researchers found that high heat and tidal circulation (flushing) has the ability to hold cysts – a potential seed stock for future blooms.  (Old Fort Pond South Hampton New York Dredging, January 5 minutes regular meeting of the Board of Trustees of the free holders and commonalty of the Town of South Hampton, New York).

Poorly flushed areas nay hold future seed banks for “toxic blooms.”

Appendix #4
Tampa Bay, Indian River and Lake Studies Lead
Nation about Sapropel-Nitrogen-Ammonia
Sapropel/Submerged Aquatic Vegetation Contain Bacterial Processes Related to Climate Cycles

In the 1950’s and 1960’s, effects of a changed water cycle in the Everglades had caused researchers to concentrate on Florida peat studies – an area that is often “hot” according to our New England standards New England was in a cold climate cycle with subzero temperatures that freeze bays and salt ponds. Here in the fisheries literature you see the results, of this New England cold strong hurricanes, thick ice and shorter growing seasons.  Seed companies faced with a shorter growing season developed the “number of days till harvest” seeking on advantage for marketing.  Seed packets sold today same reference the growing season time.

But in the 1950’s and 1960’s if you were interested in the sulfur cycle or sapropel you needed to be in Florida.  Most of the direct references to sapropel or subtidal peat – either in the formation of coal or using such wet peat for agriculture Florida was the place to be.  In fact, Florida hosted the first agricultural Peat Experiment Station in Belle Glade opening in 1923.

To fully understand sapropel you needed to look at bacteria and the formation of coal.  It is the sulfur reducing bacteria (SRB) that utilize sulfate as an oxygen source and in the process seeped hydrogen sulfide into this ooze and later fossilized is coal seams.  That is how sulfur was introduced into coal by bacteria.  To have this happen it needs to be “hot” and oxygen bacteria not present or at least then a small part of the bacterial population.  This is why coal was formed long ago when the earth was hot and sulfur was a dominant atmosphere constituent.  In fact the discussion about global warming is largely the possible return of sulfur to the loss of oxygen requiring life.  Putting sulfides into the air hurts oxygen life – it is as simple or complicated as that.

That is one of the interesting aspects of the blue crab, it is so to speak as it can carry vibrio bacteria, with little effect (it seems), while vibrio bacteria is a pathogen to many organisms (including us) the blue crab lives in an environment that fosters sulfur bacteria but has adapted to its presence.  Some research has indicated that some species have the ability to immobilize vibrio – not kill it but to make it “sticky” by changing bonding locations as to make them ineffective.  It was described to me as grease on a door knob- the door is still there but the knob has no grip and therefore cannot “be opened.”  To understand the chemistry of sapropel the explanation of this bacterial battle needs to be included.  The area of study that allows us to study this bacterial battle is the soils and peats in cold or hot periods, and Florida presents a longer grow, season for sulfur because its climate is warmer (New England has vibrio perhaps in only the hottest of times).  In cold and in oxygen containing waters sulfate reducing bacteria loose to oxygen bacteria that are energy efficient.  In heat sulfate reducing bacteria (SRO) set the habitat conditions that extend into acid conditions and sulfuric acid soils that can be part of seafood disease and parasites.  Sapropel is now considered a bank of spores and cysts that are possibly released in rapid sulfuric acids (part of the sapropel – sulfur cycle) that activate disease hosts even perhaps the dreaded oyster disease MSX.  There appears to be a correlation between storms and disease perhaps related to release of sapropel spores and cysts – the creation of acid bottoms that could activate these spores and cysts.

Appendix #5

National Oceanic and Atmospheric Administration

Northeast Fisheries Center
Sandy Hook Laboratory
Highlands, NJ  07732

September 15, 1987    F/NEC34: CMK

Mr. Timothy C. Visel
Sea Grant Advisory Program
The University of Connecticut at Avery Point
Groton, CT  06340

Dear Tim;

   I have carefully read through your report, Mitigation of Dredging Impacts to Oyster Population.  It reads as if you have researched the problem very well and have come to a reasonable conclusion.  If you have any specific questions relating to it, please let me now and I will try to answer them.

                  Sincerely yours,

                  Clyde L. MacKenzie, Jr.
                  Fishery Biologist

June 2023


The Guilford, CT Foote Farm Use of Marine Mud Sapropel on Farm Fields
New Haven Experiment Station Report (CT)
January 16, 1883
The Board of Control of The Connecticut Agriculture Experiment Station
Sample Test No. 685 Marine Mud

One of the first responsibilities of the New Haven Agriculture Experiment Station was to test and report analysis of all fertilizers – putting an end to false claims of commercial fertilizer companies that had “little honesty to spare to say the least,” according to Professor W.H. Brewer, 1874-75 in the Annual Report of the Connecticut Board of Agriculture Report of the Experiment Station on page 243.  In the scope of work that included testing natural fertilizers such as marine muds (humus – sapropel) and the account of William T. Foote of Guilford, Connecticut is one of the most detailed.  The Foote family farm encompassed the coastal Mulberry Point section of Guilford, Connecticut and like many coastal farmers in the 1880s, as the great heat intensified (1880 – 1920), sold off lots for summer cottages or camps for those wishing to escape the disease-ridden killer heat waves in cities.  (The Foote Farm would also host a fish oil factory at Indian Cove 1873 and in 1885; William Foote began selling small parcels for those families seeking the cool salt air breezes (See The Guilford Keeping Society Archives).
From the Experiment Station Report (New Haven, CT) January 16th, 1883, The Board of Control of the Connecticut Agricultural Experiment Station, Sample Test number 685 – Marine Mud – the sample was sent by William T. Foote of Guilford (page 54) – quoting William Foote’s sample  in the New Haven Agricultural Station report:

“This marine mud, compared with stable marine is as rich or richer in lime, magnesia-potash, soda and sulfuric acid. It contains but one –third as much nitrogen and is quite deficient in phosphoric acid. It would serve admirably to use in connection with fish manures which supply little besides nitrogen and phosphates.”

Mr. Foote himself writes as follows regarding this mud:

“The mud is washed into a small bay between Sachems Head and Mulberry Point (Guilford, CT – T. Visel); and is flooded at every tide. I have had fifteen years’ experience with it on light-textured through dark colored loam with a clayish subsoil or under laid by rock.  It should be dug in winter; the action of the frost pulverizes it until it is like ashes. It is then left to dry a month or so. If dug in summer, it bakes hard. I cart it to fields from twenty rods to a half-mile distant.

It costs two cents a bushel dumped on the field ready to spread. I use from 800 to 1000 bushels per acre, in drills and in hills, broadcast on pasture or spread and plowed in when I used 2000 bushels mud to the acre. I raised potatoes at the rate of 400 bushels. One car load was accidentally spread upon a space about 15 feet square and plowed in, and a very large crop was the resulting from one hill I took 13 potatoes (all there were) which weighed 5 ½ pounds.  With corn, I tried alternate rows of mud and yard manure; the latter from a yard of twenty cows were 1,100 bushels of grain had been fed in the winter.  Early in the season the mud rows did not show as well as the other, later they caught up and were equal in results to the other in size of stalk and amount of grain. Of English hay, I have 3 tons per acre where not hay, but mud has been used for years. Top-dressing pastures once in three years keeps them in fine grass and apparently would do so forever. I don’t find it quick enough for an early vegetable garden, without some more heating manure with beets, I have carried 900 to 1000 bushels per acre.”



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